bims-auttor 2021-03-21 papers

bims-auttor

Biomed News

on Autophagy and mTOR

Issue of 2021–03–21
34 papers selected by
Viktor Korolchuk, Newcastle University

AMPK-dependent phosphorylation is required for transcriptional activation of TFEB and TFE3.
Autophagy facilitates mitochondrial rebuilding after acute heat stress via a DRP-1-dependent process.
NAD+ supplementation prevents STING-induced senescence in ataxia telangiectasia by improving mitophagy.
PI3K/AKT/MTOR and ERK1/2-MAPK signaling pathways are involved in autophagy stimulation induced by caloric restriction or caloric restriction mimetics in cortical neurons.
Atg9-centered multi-omics integration reveals new autophagy regulators in Saccharomyces cerevisiae.
Selective Autophagy Tolerates Symbiotic Bacteria in the Drosophila Intestine.
Mitophagy: An Emerging Target in Ocular Pathology.
Exogenous Alpha-Synuclein Evoked Parkin Downregulation Promotes Mitochondrial Dysfunction in Neuronal Cells. Implications for Parkinson's Disease Pathology.
Lysosomes and Cancer Progression: A Malignant Liaison.
VCP/p97 modulates PtdIns3P production and autophagy initiation.
PGC-1α alleviates mitochondrial dysfunction via TFEB-mediated autophagy in cisplatin-induced acute kidney injury.
Hsp90-mediated regulation of DYRK3 couples stress granule disassembly and growth via mTORC1 signaling.
α-Catenin levels determine direction of YAP/TAZ response to autophagy perturbation.
Sorting nexin Mdm1/SNX14 regulates nucleolar dynamics at the NVJ after TORC1 inactivation.
Estrogen Plays a Crucial Role in Rab9-Dependent Mitochondrial Autophagy, Delaying Arterial Senescence.
The Macroautophagy Machinery in MHC Restricted Antigen Presentation.
Autophagy mediated lipid catabolism facilitates glioma progression to overcome bioenergetic crisis.
A fluorescent nanoprobe based on cell-penetrating peptides and quantum dots for ratiometric monitoring of pH fluctuation in lysosomes.
Perspectives on Organelle Interaction, Protein Dysregulation, and Cancer Disease.
PKA compartmentalization links cAMP signaling and autophagy.
Mitophagy in Pancreatic Cancer.
AMPK inhibits mTOR-driven keratinocyte proliferation after skin damage and stress.
CREG1 improves the capacity of the skeletal muscle response to exercise endurance via modulation of mitophagy.
Involvement of Mitochondrial Dynamics and Mitophagy in Sevoflurane-Induced Cell Toxicity.
TEX264 at the intersection of autophagy and DNA repair.
Characterization of a natural variant of human NDP52 and its functional consequences on mitophagy.
A Guide To… The Regulation Of Selective Autophagy Receptors.
Mitophagy protein PINK1 suppresses colon tumor growth by metabolic reprogramming via p53 activation and reducing acetyl-CoA production.
Inhibition of mTOR signaling by genetic removal of p70 S6 kinase 1 increases anxiety-like behavior in mice.
Molecular basis of V-ATPase inhibition by bafilomycin A1.
Selective autophagy receptor SQSTM1/ p62 inhibits Seneca Valley virus replication by targeting viral VP1 and VP3.
Rheb mediates neuronal-activity-induced mitochondrial energetics through mTORC1-independent PDH activation.
Mechanobiology of Autophagy: The Unexplored Side of Cancer.
Reduced nicotinamide mononucleotide is a new and potent NAD+ precursor in mammalian cells and mice.

Autophagy. 2021 Mar 18. 1-19

AMPK-dependent phosphorylation is required for transcriptional activation of TFEB and TFE3.

Mathieu Paquette, Leeanna El-Houjeiri, Linda C Zirden, Pietri Puustinen, Paola Blanchette, Hyeonju Jeong, Kurt Dejgaard, Peter M Siegel, Arnim Pause.

  Increased macroautophagy/autophagy and lysosomal activity promote tumor growth, survival and chemo-resistance. During acute starvation, autophagy is rapidly engaged by AMPK (AMP-activated protein kinase) activation and MTOR (mechanistic target of rapamycin kinase) complex 1 (MTORC1) inhibition to maintain energy homeostasis and cell survival. TFEB (transcription factor E3) and TFE3 (transcription factor binding to IGHM enhancer 3) are master transcriptional regulators of autophagy and lysosomal activity and their cytoplasm/nuclear shuttling is controlled by MTORC1-dependent multisite phosphorylation. However, it is not known whether and how the transcriptional activity of TFEB or TFE3 is regulated. We show that AMPK mediates phosphorylation of TFEB and TFE3 on three serine residues, leading to TFEB and TFE3 transcriptional activity upon nutrient starvation, FLCN (folliculin) depletion and pharmacological manipulation of MTORC1 or AMPK. Collectively, we show that MTORC1 specifically controls TFEB and TFE3 cytosolic retention, whereas AMPK is essential for TFEB and TFE3 transcriptional activity. This dual and opposing regulation of TFEB and TFE3 by MTORC1 and AMPK is reminiscent of the regulation of another critical regulator of autophagy, ULK1 (unc-51 like autophagy activating kinase 1). Surprisingly, we show that chemoresistance is mediated by AMPK-dependent activation of TFEB, which is abolished by pharmacological inhibition of AMPK or mutation of serine 466, 467 and 469 to alanine residues within TFEB. Altogether, we show that AMPK is a key regulator of TFEB and TFE3 transcriptional activity, and we validate AMPK as a promising target in cancer therapy to evade chemotherapeutic resistance.AbbreviationsACACA: acetyl-CoA carboxylase alpha; ACTB: actin beta; AICAR: 5-aminoimidazole-4-carboxamide ribonucleotide; AMPK: AMP-activated protein kinase; AMPKi: AMPK inhibitor, SBI-0206965; CA: constitutively active; CARM1: coactivator-associated arginine methyltransferase 1; CFP: cyan fluorescent protein; CLEAR: coordinated lysosomal expression and regulation; DKO: double knock-out; DMEM: Dulbecco's modified Eagle's medium; DMSO: dimethyl sulfoxide; DQ-BSA: self-quenched BODIPY® dye conjugates of bovine serum albumin; EBSS: Earle's balanced salt solution; FLCN: folliculin; GFP: green fluorescent protein; GST: glutathione S-transferases; HD: Huntington disease; HTT: huntingtin; KO: knock-out; LAMP1: lysosomal associated membrane protein 1; MEF: mouse embryonic fibroblasts; MITF: melanocyte inducing transcription factor; MTORC1: MTOR complex 1; PolyQ: polyglutamine; RPS6: ribosomal protein S6; RT-qPCR: reverse transcription quantitative polymerase chain reaction; TCL: total cell lysates; TFE3: transcription factor binding to IGHM enhancer 3; TFEB: transcription factor EB; TKO: triple knock-out; ULK1: unc-51 like autophagy activating kinase 1.

Keywords:  AMP-activated protein kinase; autophagy; drug resistance; lysosomal biogenesis; mechanistic target of rapamycin kinase; phosphorylation; transcription factor E3; transcription factor EB

DOI:  https://doi.org/10.1080/15548627.2021.1898748
J Cell Biol. 2021 Apr 05. pii: e201909139. [Epub ahead of print]220(4):

Autophagy facilitates mitochondrial rebuilding after acute heat stress via a DRP-1-dependent process.

Yanfang Chen, Romane Leboutet, Céline Largeau, Siham Zentout, Christophe Lefebvre, Agnès Delahodde, Emmanuel Culetto, Renaud Legouis.

Acute heat stress (aHS) can induce strong developmental defects in Caenorhabditis elegans larva but not lethality or sterility. This stress results in transitory fragmentation of mitochondria, formation of aggregates in the matrix, and decrease of mitochondrial respiration. Moreover, active autophagic flux associated with mitophagy events enables the rebuilding of the mitochondrial network and developmental recovery, showing that the autophagic response is protective. This adaptation to aHS does not require Pink1/Parkin or the mitophagy receptors DCT-1/NIX and FUNDC1. We also find that mitochondria are a major site for autophagosome biogenesis in the epidermis in both standard and heat stress conditions. In addition, we report that the depletion of the dynamin-related protein 1 (DRP-1) affects autophagic processes and the adaptation to aHS. In drp-1 animals, the abnormal mitochondria tend to modify their shape upon aHS but are unable to achieve fragmentation. Autophagy is induced, but autophagosomes are abnormally elongated and clustered on mitochondria. Our data support a role for DRP-1 in coordinating mitochondrial fission and autophagosome biogenesis in stress conditions.

DOI: https://doi.org/10.1083/jcb.201909139
Aging Cell. 2021 Mar 18. e13329

NAD+ supplementation prevents STING-induced senescence in ataxia telangiectasia by improving mitophagy.

Beimeng Yang, Xiuli Dan, Yujun Hou, Jong-Hyuk Lee, Noah Wechter, Sudarshan Krishnamurthy, Risako Kimura, Mansi Babbar, Tyler Demarest, Ross McDevitt, Shiliang Zhang, Yongqing Zhang, Mark P Mattson, Deborah L Croteau, Vilhelm A Bohr.

  Senescence phenotypes and mitochondrial dysfunction are implicated in aging and in premature aging diseases, including ataxia telangiectasia (A-T). Loss of mitochondrial function can drive age-related decline in the brain, but little is known about whether improving mitochondrial homeostasis alleviates senescence phenotypes. We demonstrate here that mitochondrial dysfunction and cellular senescence with a senescence-associated secretory phenotype (SASP) occur in A-T patient fibroblasts, and in ATM-deficient cells and mice. Senescence is mediated by stimulator of interferon genes (STING) and involves ectopic cytoplasmic DNA. We further show that boosting intracellular NAD+ levels with nicotinamide riboside (NR) prevents senescence and SASP by promoting mitophagy in a PINK1-dependent manner. NR treatment also prevents neurodegeneration, suppresses senescence and neuroinflammation, and improves motor function in Atm-/- mice. Our findings suggest a central role for mitochondrial dysfunction-induced senescence in A-T pathogenesis, and that enhancing mitophagy as a potential therapeutic intervention.

Keywords:  Ataxia Telangiectasia; Nicotinamide riboside; SASP; mitophagy; senescence

DOI:  https://doi.org/10.1111/acel.13329
Aging (Albany NY). 2021 Mar 14. 13

PI3K/AKT/MTOR and ERK1/2-MAPK signaling pathways are involved in autophagy stimulation induced by caloric restriction or caloric restriction mimetics in cortical neurons.

Marisa Ferreira-Marques, André Carvalho, Cláudia Cavadas, Célia A Aveleira.

  Caloric restriction has been shown to robustly ameliorate age-related diseases and to prolong lifespan in several model organisms, and these beneficial effects are dependent on the stimulation of autophagy. Autophagy dysfunction contributes to the accumulation of altered macromolecules, and is a key mechanism of promoting aging and age-related disorders, as neurodegenerative ones. We have previously shown that caloric restriction (CR), and CR mimetics Neuropeptide Y (NPY) and ghrelin, stimulate autophagy in rat cortical neurons, however by unknown molecular mechanisms. Overall, we show that CR, NPY, and ghrelin stimulate autophagy through PI3K/AKT/MTOR inhibition and ERK1/2-MAPK activation. The knowledge of these kinases in autophagy regulation and the contribution to the understanding of molecular mechanism facilitates the discovery of more targeted therapeutic strategies to stimulate autophagy, which is relevant in the context of age-related disorders.

Keywords:  aging; autophagy; caloric restriction mimetics; cortical neurons

DOI:  https://doi.org/10.18632/aging.202805
Autophagy. 2021 Mar 15. 1-24

Atg9-centered multi-omics integration reveals new autophagy regulators in Saccharomyces cerevisiae.

Di Peng, Chen Ruan, Shanshan Fu, Chengwen He, Jingzhen Song, Hui Li, Yiran Tu, Dachao Tang, Lan Yao, Shaofeng Lin, Ying Shi, Weizhi Zhang, Hao Zhou, Le Zhu, Cong Ma, Cheng Chang, Jie Ma, Zhiping Xie, Chenwei Wang, Yu Xue.

  In Saccharomyces cerevisiae, Atg9 is an important autophagy-related (Atg) protein, and interacts with hundreds of other proteins. How many Atg9-interacting proteins are involved in macroautophagy/autophagy is unclear. Here, we conducted a multi-omic profiling of Atg9-dependent molecular landscapes during nitrogen starvation-induced autophagy, and identified 290 and 256 genes to be markedly regulated by ATG9 in transcriptional and translational levels, respectively. Unexpectedly, we found most of known Atg proteins and autophagy regulators that interact with Atg9 were not significantly changed in the mRNA or protein level during autophagy. Based on a hypothesis that proteins with similar molecular characteristics might have similar functions, we developed a new method named inference of functional interacting partners (iFIP) to integrate the transcriptomic, proteomic and interactomic data, and predicted 42 Atg9-interacting proteins to be potentially involved in autophagy, including 15 known Atg proteins or autophagy regulators. We validated 2 Atg9-interacting partners, Glo3 and Scs7, to be functional in both bulk and selective autophagy. The mRNA and protein expressions but not subcellular localizations of Glo3 and Scs7 were affected with or without ATG9 during autophagy, whereas the colocalizations of the 2 proteins and Atg9 were markedly enhanced at early stages of the autophagic process. Further analyses demonstrated that Glo3 but not Scs7 regulates the retrograde transport of Atg9 during autophagy. A working model was illustrated to highlight the importance of the Atg9 interactome. Taken together, our study not only provided a powerful method for analyzing the multi-omics data, but also revealed 2 new players that regulate autophagy.Abbreviations: ALP: alkaline phosphatase; Arf1: ADP-ribosylation factor 1; Atg: autophagy-related; Co-IP: co-immunoprecipitation; Cvt: cytoplasm-to-vacuole targeting; DEM: differentially expressed mRNA; DEP: differentially expressed protein; DIC: differential interference contrast; E-ratio: enrichment ratio; ER: endoplasmic reticulum; ES: enrichment score; FC: fold change; FPKM: fragments per kilobase of exon per million fragments mapped; GAP: GTPase-activating protein; GFP: green fluorescent protein; GO: gene ontology; GSEA: gene set enrichment analysis; GST: glutathione S-transferase; HA: hemagglutinin; iFIP: inference of functional interacting partners; KO: knockout; LR: logistic regression; OE: over-expression; PAS: phagophore assembly site; PPI: protein-protein interaction; RFP: red fluorescence protein; RNA-seq: RNA sequencing; RT-PCR: real-time polymerase chain reaction; SCC: Spearman's correlation coefficient; SD-N: synthetic minimal medium lacking nitrogen; THANATOS: The Autophagy, Necrosis, ApopTosis OrchestratorS; Vsn: variance stabilization normalization; WT: wild-type.

Keywords:  Atg9; atg9 interactome; autophagy; proteomics; transcriptomics

DOI:  https://doi.org/10.1080/15548627.2021.1898749
Autophagy. 2021 Mar 18.

Selective Autophagy Tolerates Symbiotic Bacteria in the Drosophila Intestine.

Hiroki Nagai, Tamaki Yano.

  Intestinal epithelia functions as a barrier to protect the host from environmental microbes. Defects in macroautophagy/autophagy combined with intestinal microbes cause a disruption of homeostasis of the tissue, which is associated with the etiology of Crohn disease, an inflammatory bowel disease. However, the molecular mechanism of how autophagy interacts with microbes in the pathology are mostly unrevealed. Our recent findings using Drosophila as a model system showed that autophagy in enterocytes suppresses a regenerative response triggered by reactive oxygen species (ROS) secreted by the host epithelia towards commensal bacteria in the intestine. Without this suppression, accumulation of a receptor protein of selective autophagy, ref(2)P, continuously acts as a signaling platform to cause excessive regeneration via cytokine production by yki (yorkie) activation. This chronic response leads to the acceleration of age-dependent barrier dysfunction, systemic inflammation, and shorter lifespan. These results uncover a novel regulatory network linking commensal bacteria, autophagy, and gut homeostasis, represented by ROS, ref(2)P, and the hippo pathway.

Keywords:  Age-related barrier dysfunction; Drosophila; hippo pathway; host-microbe interaction; intestinal regeneration; ref(2)P/p62; selective autophagy; symbiotic bacteria

DOI:  https://doi.org/10.1080/15548627.2021.1904490
Invest Ophthalmol Vis Sci. 2021 Mar 01. 62(3): 22

Mitophagy: An Emerging Target in Ocular Pathology.

Jessica M Skeie, Darryl Y Nishimura, Cheryl L Wang, Gregory A Schmidt, Benjamin T Aldrich, Mark A Greiner.

Mitochondrial function is essential for the viability of aerobic eukaryotic cells, as mitochondria provide energy through the generation of adenosine triphosphate (ATP), regulate cellular metabolism, provide redox balancing, participate in immune signaling, and can initiate apoptosis. Mitochondria are dynamic organelles that participate in a cyclical and ongoing process of regeneration and autophagy (clearance), termed mitophagy specifically for mitochondrial (macro)autophagy. An imbalance in mitochondrial function toward mitochondrial dysfunction can be catastrophic for cells and has been characterized in several common ophthalmic diseases. In this article, we review mitochondrial homeostasis in detail, focusing on the balance of mitochondrial dynamics including the processes of fission and fusion, and provide a description of the mechanisms involved in mitophagy. Furthermore, this article reviews investigations of ocular diseases with impaired mitophagy, including Fuchs endothelial corneal dystrophy, primary open-angle glaucoma, diabetic retinopathy, and age-related macular degeneration, as well as several primary mitochondrial diseases with ocular phenotypes that display impaired mitophagy, including mitochondrial encephalopathy lactic acidosis stroke, Leber hereditary optic neuropathy, and chronic progressive external ophthalmoplegia. The results of various studies using cell culture, animal, and human tissue models are presented and reflect a growing awareness of mitophagy impairment as an important feature of ophthalmic disease pathology. As this review indicates, it is imperative that mitophagy be investigated as a targetable mechanism in developing therapies for ocular diseases characterized by oxidative stress and mitochondrial dysfunction.

DOI: https://doi.org/10.1167/iovs.62.3.22
Front Aging Neurosci. 2021 ;13 591475

Exogenous Alpha-Synuclein Evoked Parkin Downregulation Promotes Mitochondrial Dysfunction in Neuronal Cells. Implications for Parkinson's Disease Pathology.

Anna Wilkaniec, Anna M Lenkiewicz, Lidia Babiec, Emilia Murawska, Henryk M Jęśko, Magdalena Cieślik, Carsten Culmsee, Agata Adamczyk.

  Aberrant secretion and accumulation of α-synuclein (α-Syn) as well as the loss of parkin function are associated with the pathogenesis of Parkinson's disease (PD). Our previous study suggested a functional interaction between those two proteins, showing that the extracellular α-Syn evoked post-translational modifications of parkin, leading to its autoubiquitination and degradation. While parkin plays an important role in mitochondrial biogenesis and turnover, including mitochondrial fission/fusion as well as mitophagy, the involvement of parkin deregulation in α-Syn-induced mitochondrial damage is largely unknown. In the present study, we demonstrated that treatment with exogenous α-Syn triggers mitochondrial dysfunction, reflected by the depolarization of the mitochondrial membrane, elevated synthesis of the mitochondrial superoxide anion, and a decrease in cellular ATP level. At the same time, we observed a protective effect of parkin overexpression on α-Syn-induced mitochondrial dysfunction. α-Syn-dependent disturbances of mitophagy were also shown to be directly related to reduced parkin levels in mitochondria and decreased ubiquitination of mitochondrial proteins. Also, α-Syn impaired mitochondrial biosynthesis due to the parkin-dependent reduction of PGC-1α protein levels. Finally, loss of parkin function as a result of α-Syn treatment induced an overall breakdown of mitochondrial homeostasis that led to the accumulation of abnormal mitochondria. These findings may thus provide the first compelling evidence for the direct association of α-Syn-mediated parkin depletion to impaired mitochondrial function in PD. We suggest that improvement of parkin function may serve as a novel therapeutic strategy to prevent mitochondrial impairment and neurodegeneration in PD (thereby slowing the progression of the disease).

Keywords:  PGC-1 alpha; Parkinson’s disease; mitochondria dysfunction; mitophagy; parkin; α-synuclein (α-syn)

DOI:  https://doi.org/10.3389/fnagi.2021.591475
Front Cell Dev Biol. 2021 ;9 642494

Lysosomes and Cancer Progression: A Malignant Liaison.

Eda R Machado, Ida Annunziata, Diantha van de Vlekkert, Gerard C Grosveld, Alessandra d'Azzo.

  During primary tumorigenesis isolated cancer cells may undergo genetic or epigenetic changes that render them responsive to additional intrinsic or extrinsic cues, so that they enter a transitional state and eventually acquire an aggressive, metastatic phenotype. Among these changes is the alteration of the cell metabolic/catabolic machinery that creates the most permissive conditions for invasion, dissemination, and survival. The lysosomal system has emerged as a crucial player in this malignant transformation, making this system a potential therapeutic target in cancer. By virtue of their ubiquitous distribution in mammalian cells, their multifaced activities that control catabolic and anabolic processes, and their interplay with other organelles and the plasma membrane (PM), lysosomes function as platforms for inter- and intracellular communication. This is due to their capacity to adapt and sense nutrient availability, to spatially segregate specific functions depending on their position, to fuse with other compartments and with the PM, and to engage in membrane contact sites (MCS) with other organelles. Here we review the latest advances in our understanding of the role of the lysosomal system in cancer progression. We focus on how changes in lysosomal nutrient sensing, as well as lysosomal positioning, exocytosis, and fusion perturb the communication between tumor cells themselves and between tumor cells and their microenvironment. Finally, we describe the potential impact of MCS between lysosomes and other organelles in propelling cancer growth and spread.

Keywords:  cancer progression; lysosomal exocytosis; lysosomal membrane contact sites; lysosome movement; lysosome positioning

DOI:  https://doi.org/10.3389/fcell.2021.642494
Autophagy. 2021 Mar 09. 1-2

VCP/p97 modulates PtdIns3P production and autophagy initiation.

Lidia Wrobel, Sandra M Hill, Avraham Ashkenazi, David C Rubinsztein.

  VCP/p97 is an essential multifunctional protein implicated in a plethora of intracellular quality control systems, and abnormal function of VCP is the underlying cause of several neurodegenerative disorders. We reported that VCP regulates the levels of the macroautophagy/autophagy-inducing lipid phosphatidylinositol-3-phosphate (PtdIns3P) by modulating the activity of the BECN1 (beclin 1)-containing phosphatidylinositol 3-kinase (PtdIns3K) complex. VCP stimulates the deubiquitinase activity of ATXN3 (ataxin 3) to stabilize BECN1 protein levels and also interacts with and promotes the assembly and kinase activity of the PtdIns3K complex. Acute inhibition of VCP activity impairs autophagy induction, demonstrated by a diminished PtdIns3P production and decreased recruitment of early autophagy markers WIPI2 and ATG16L1. Thus, VCP promotes autophagosome biogenesis, in addition to its previously described role in autophagosome maturation.

Keywords:  ATXN3; PI(3)P; PI3K; VCP/p97; autophagy initiation; beclin 1

DOI:  https://doi.org/10.1080/15548627.2021.1898742
Aging (Albany NY). 2021 Mar 10. 13

PGC-1α alleviates mitochondrial dysfunction via TFEB-mediated autophagy in cisplatin-induced acute kidney injury.

Longhui Yuan, Yujia Yuan, Fei Liu, Lan Li, Jingping Liu, Younan Chen, Jingqiu Cheng, Yanrong Lu.

  Because of the key role of impaired mitochondria in the progression of acute kidney injury (AKI), it is striking that peroxisome proliferator γ coactivator 1-α (PGC-1α), a transcriptional coactivator of genes involved in mitochondrial biogenesis and autophagy, protects from kidney injury. However, the specific mechanism involved in PGC-1α-mediated autophagy remains elusive. In vivo, along with the severe kidney damage, the expression of PGC-1α was decreased in cisplatin-induced AKI mice. Conversely, PGC-1α activator (ZLN005) administration could alleviate kidney injury. Consistently, in vitro overexpression of PGC-1α or ZLN005 treatment inhibited cell apoptosis and mitochondrial dysfunction induced by cisplatin. Moreover, ZLN005 treatment increased the expression of LC3-II and co-localization between LC3 and mitochondria, suggesting that the mitophagy was activated. Furthermore, PGC-1α-mediated the activation of mitophagy was reliant on the increased expression of TFEB, and the protective effects were abrogated in TFEB-knockdown cells. These data suggest that the activation of PGC-1α could alleviate mitochondrial dysfunction and kidney injury in AKI mice via TFEB-mediated autophagy.

Keywords:  PGC-1α; TFEB; acute kidney injury; autophagy; mitochondrial dysfunction

DOI:  https://doi.org/10.18632/aging.202653
EMBO Rep. 2021 Mar 19. e51740

Hsp90-mediated regulation of DYRK3 couples stress granule disassembly and growth via mTORC1 signaling.

Laura Mediani, Francesco Antoniani, Veronica Galli, Jonathan Vinet, Arianna Dorotea Carrà, Ilaria Bigi, Vadreenath Tripathy, Tatiana Tiago, Marco Cimino, Giuseppina Leo, Triana Amen, Daniel Kaganovich, Cristina Cereda, Orietta Pansarasa, Jessica Mandrioli, Priyanka Tripathi, Dirk Troost, Eleonora Aronica, Johannes Buchner, Anand Goswami, Jared Sterneckert, Simon Alberti, Serena Carra.

  Stress granules (SGs) are dynamic condensates associated with protein misfolding diseases. They sequester stalled mRNAs and signaling factors, such as the mTORC1 subunit raptor, suggesting that SGs coordinate cell growth during and after stress. However, the molecular mechanisms linking SG dynamics and signaling remain undefined. We report that the chaperone Hsp90 is required for SG dissolution. Hsp90 binds and stabilizes the dual-specificity tyrosine-phosphorylation-regulated kinase 3 (DYRK3) in the cytosol. Upon Hsp90 inhibition, DYRK3 dissociates from Hsp90 and becomes inactive. Inactive DYRK3 is subjected to two different fates: it either partitions into SGs, where it is protected from irreversible aggregation, or it is degraded. In the presence of Hsp90, DYRK3 is active and promotes SG disassembly, restoring mTORC1 signaling and translation. Thus, Hsp90 links stress adaptation and cell growth by regulating the activity of a key kinase involved in condensate disassembly and translation restoration.

Keywords:  DYRK3; FUS-ALS; Hsp90; phase separation; stress granules

DOI:  https://doi.org/10.15252/embr.202051740
Nat Commun. 2021 03 17. 12(1): 1703

α-Catenin levels determine direction of YAP/TAZ response to autophagy perturbation.

Mariana Pavel, So Jung Park, Rebecca A Frake, Sung Min Son, Marco M Manni, Carla F Bento, Maurizio Renna, Thomas Ricketts, Fiona M Menzies, Radu Tanasa, David C Rubinsztein.

The factors regulating cellular identity are critical for understanding the transition from health to disease and responses to therapies. Recent literature suggests that autophagy compromise may cause opposite effects in different contexts by either activating or inhibiting YAP/TAZ co-transcriptional regulators of the Hippo pathway via unrelated mechanisms. Here, we confirm that autophagy perturbation in different cell types can cause opposite responses in growth-promoting oncogenic YAP/TAZ transcriptional signalling. These apparently contradictory responses can be resolved by a feedback loop where autophagy negatively regulates the levels of α-catenins, LC3-interacting proteins that inhibit YAP/TAZ, which, in turn, positively regulate autophagy. High basal levels of α-catenins enable autophagy induction to positively regulate YAP/TAZ, while low α-catenins cause YAP/TAZ activation upon autophagy inhibition. These data reveal how feedback loops enable post-transcriptional determination of cell identity and how levels of a single intermediary protein can dictate the direction of response to external or internal perturbations.

DOI: https://doi.org/10.1038/s41467-021-21882-1
Biochem Biophys Res Commun. 2021 Mar 16. pii: S0006-291X(21)00416-2. [Epub ahead of print]552 1-8

Sorting nexin Mdm1/SNX14 regulates nucleolar dynamics at the NVJ after TORC1 inactivation.

Tasnuva Sharmin, Tsuneyuki Takuma, Shamsul Morshed, Takashi Ushimaru.

  The degradation of nucleolar proteins - nucleophagy - is elicited by nutrient starvation or the inactivation of target of rapamycin complex 1 (TORC1) protein kinase in budding yeast. Prior to nucleophagy, nucleolar proteins migrate to the nucleus-vacuole junction (NVJ), where micronucleophagy occurs, whereas rDNA (rRNA gene) repeat regions are condensed and escape towards NVJ-distal sites. This suggests that the NVJ controls nucleolar dynamics from outside of the nucleus after TORC1 inactivation, but its molecular mechanism is unclear. Here, we show that sorting nexin (SNX) Mdm1, an inter-organelle tethering protein at the NVJ, mediates TORC1 inactivation-induced nucleolar dynamics. Furthermore, Mdm1 was required for proper nucleophagic degradation of nucleolar proteins after TORC1 inactivation, where it was dispensable for the induction of nucleophagic flux itself. This indicated that nucleophagy and nucleolar dynamics are independently regulated by TORC1 inactivation. Finally, Mdm1 was critical for survival during nutrient starvation conditions. Mutations of SNX14, a human Mdm1 homolog, cause neurodevelopmental disorders. This study provides a novel insight into relationship between sorting nexin-mediated microautophagy and neurodevelopmental disorders.

Keywords:  Mdm1; NVJ; Nucleophagy; SNX14; TORC1; rDNA

DOI:  https://doi.org/10.1016/j.bbrc.2021.03.033
J Am Heart Assoc. 2021 Mar 15. e019310

Estrogen Plays a Crucial Role in Rab9-Dependent Mitochondrial Autophagy, Delaying Arterial Senescence.

Yuichi Sasaki, Yoshiyuki Ikeda, Yoshihiro Uchikado, Yuichi Akasaki, Junichi Sadoshima, Mitsuru Ohishi.

  Background The risk of cardiovascular disease is known to increase after menopause. Mitochondria, which undergo quality control via mitochondrial autophagy, play a crucial role in the regulation of cellular senescence. The aim of this study was to investigate whether the effect of estrogen-mediated protection from senescence on arteries is attributed to the induction of mitochondrial autophagy. Methods and Results We used human umbilical vein cells, vascular smooth muscle cells, and 12-week-old female C57BL/6 mice. The administration of 17β-estradiol (E2) to cells inhibited cellular senescence and mitochondrial dysfunction. Furthermore, E2 increased mitochondrial autophagy, maintaining mitochondrial function, and retarding cellular senescence. Of note, E2 did not modulate LC3 (light chain 3), and ATG7 (autophagy related 7) deficiency did not suppress mitochondrial autophagy in E2-treated cells. Conversely, E2 increased the colocalization of Rab9 with LAMP2 (lysosomal-associated membrane protein 2) signals. The E2-mediated effects on mitochondrial autophagy were abolished by the knockdown of either Ulk1 or Rab9. These results suggest that E2-mediated mitochondrial autophagy is associated with Rab9-dependent alternative autophagy. E2 upregulated SIRT1 (sirtuin 1) and activated LKB1 (liver kinase B1), AMPK (adenosine monophosphate-activated protein kinase), and Ulk1, indicating that the effect of E2 on the induction of Rab9-dependent alternative autophagy is mediated by the SIRT1/LKB1/AMPK/Ulk1 pathway. Compared with the sham-operated mice, ovariectomized mice showed reduced mitochondrial autophagy and accelerated mitochondrial dysfunction and arterial senescence; these detrimental alterations were successfully rescued by the administration of E2. Conclusions We showed that E2-induced mitochondrial autophagy plays a crucial role in the delay of vascular senescence. The Rab9-dependent alternative autophagy is behind E2-induced mitochondrial autophagy.

Keywords:  autophagy; estrogen; mitochondria; vascular senescence

DOI:  https://doi.org/10.1161/JAHA.120.019310
Front Immunol. 2021 ;12 628429

The Macroautophagy Machinery in MHC Restricted Antigen Presentation.

Christian Münz.

  Autophagy-related (ATG) gene products regulate macroautophagy, LC3-associated phagocytosis (LAP) and LC3-dependent extracellular vesicle loading and secretion (LDELS). These processes also influence antigen processing for presentation on major histocompatibility complex (MHC) molecules to T cells. Here, I summarize how these different pathways use the macroautophagy machinery, contribute to MHC class I and II restricted antigen presentation and influence autoimmunity, tumor immunology and immune control of infectious diseases. Targeting these different pathways should allow the regulation of intracellular and extracellular antigen presentation to T cells to modulate protective and pathological immune responses.

Keywords:  LC3-associated phagocytosis; cross-presentation; cytotoxic CD8+ T cells; exocytosis; helper CD4+ T cells

DOI:  https://doi.org/10.3389/fimmu.2021.628429
Br J Cancer. 2021 Mar 15.

Autophagy mediated lipid catabolism facilitates glioma progression to overcome bioenergetic crisis.

Chenran Wang, Michael A Haas, Syn Kok Yeo, Ritama Paul, Fuchun Yang, Subrahmanya Vallabhapurapu, Xiaoyang Qi, David R Plas, Jun-Lin Guan.

BACKGROUND: Activation of mTORC1 plays a significant role in cancer development and progression. However, the metabolic mechanisms to sustain mTORC1 activation of cancer cells within stressed environments are still under-appreciated. We recently revealed high autophagy activity in tumour cells with mTORC1 hyper-activation. Nevertheless, the functions and mechanisms of autophagy in regulating mTORC1 in glioma are not studied.
METHODS: Using glioma patient database and human glioma cells, we assessed the mechanisms and function of selective autophagy to sustain mTORC1 hyper-activation in glioma.
RESULTS: We revealed a strong association of altered mRNA levels in mTORC1 upstream and downstream genes with prognosis of glioma patients. Our results indicated that autophagy-mediated lipid catabolism was essential to sustain mTORC1 activity in glioma cells under energy stresses. We found that autophagy inhibitors or fatty acid oxidation (FAO) inhibitors in combination with 2-Deoxy-D-glucose (2DG) decreased energy production and survival of glioma cells in vitro. Consistently, inhibition of autophagy or FAO inhibitors with 2DG effectively suppressed the progression of xenografted glioma with hyper-activated mTORC1.
CONCLUSIONS: This study established an autophagy/lipid degradation/FAO/ATP generation pathway, which might be used in brain cancer cells under energy stresses to maintain high mTORC1 signalling for tumour progression.

DOI: https://doi.org/10.1038/s41416-021-01294-0
Talanta. 2021 May 15. pii: S0039-9140(21)00129-6. [Epub ahead of print]227 122208

A fluorescent nanoprobe based on cell-penetrating peptides and quantum dots for ratiometric monitoring of pH fluctuation in lysosomes.

Yan Yang, Rui Li, Sichun Zhang, Xinrong Zhang.

  A lysosome-targeting ratiometric fluorescent nanoprobe based on cell-penetrating peptides (CPPs) and quantum dots (QDs) has been developed for monitoring pH fluctuation in living cells. The as-prepared nanoprobe is constructed by Rhodamine B labeled R9RGD CPPs as H+ response unit and the red fluorescent QDs as reference unit to achieve ratiometric pH measurement. With the help of RhB-R9RGD CPPs, the nanoprobe efficiently stains lysosomes and enables discernment of lysosomal pH fluctuation in cells treated with different pH buffers and drug stimulation. The method of using dye labeled CPPs to realize functionalization of nanoparticle in one-step reported herein is expected to obtain wider applications in the detection of subcellular active substances by combining different small molecular probes and functional peptides.

Keywords:  Cell-penetrating peptides; Lysosome-targeting; Quantum dots; Ratiometric; pH nanoprobe

DOI:  https://doi.org/10.1016/j.talanta.2021.122208
Front Cell Dev Biol. 2021 ;9 613336

Perspectives on Organelle Interaction, Protein Dysregulation, and Cancer Disease.

Paula Díaz, Alejandra Sandoval-Bórquez, Roberto Bravo-Sagua, Andrew F G Quest, Sergio Lavandero.

  In recent decades, compelling evidence has emerged showing that organelles are not static structures but rather form a highly dynamic cellular network and exchange information through membrane contact sites. Although high-throughput techniques facilitate identification of novel contact sites (e.g., organelle-organelle and organelle-vesicle interactions), little is known about their impact on cellular physiology. Moreover, even less is known about how the dysregulation of these structures impacts on cellular function and therefore, disease. Particularly, cancer cells display altered signaling pathways involving several cell organelles; however, the relevance of interorganelle communication in oncogenesis and/or cancer progression remains largely unknown. This review will focus on organelle contacts relevant to cancer pathogenesis. We will highlight specific proteins and protein families residing in these organelle-interfaces that are known to be involved in cancer-related processes. First, we will review the relevance of endoplasmic reticulum (ER)-mitochondria interactions. This section will focus on mitochondria-associated membranes (MAMs) and particularly the tethering proteins at the ER-mitochondria interphase, as well as their role in cancer disease progression. Subsequently, the role of Ca2+ at the ER-mitochondria interphase in cancer disease progression will be discussed. Members of the Bcl-2 protein family, key regulators of cell death, also modulate Ca2+ transport pathways at the ER-mitochondria interphase. Furthermore, we will review the role of ER-mitochondria communication in the regulation of proteostasis, focusing on the ER stress sensor PERK (PRKR-like ER kinase), which exerts dual roles in cancer. Second, we will review the relevance of ER and mitochondria interactions with other organelles. This section will focus on peroxisome and lysosome organelle interactions and their impact on cancer disease progression. In this context, the peroxisome biogenesis factor (PEX) gene family has been linked to cancer. Moreover, the autophagy-lysosome system is emerging as a driving force in the progression of numerous human cancers. Thus, we will summarize our current understanding of the role of each of these organelles and their communication, highlighting how alterations in organelle interfaces participate in cancer development and progression. A better understanding of specific organelle communication sites and their relevant proteins may help to identify potential pharmacological targets for novel therapies in cancer control.

Keywords:  cancer; endoplasmic reticulum; interorganelle communication; lysosome; mitochondria; peroxisome

DOI:  https://doi.org/10.3389/fcell.2021.613336
Cell Death Differ. 2021 Mar 19.

PKA compartmentalization links cAMP signaling and autophagy.

Francesca Grisan, Liliana F Iannucci, Nicoletta C Surdo, Andrea Gerbino, Sofia Zanin, Giulietta Di Benedetto, Tullio Pozzan, Konstantinos Lefkimmiatis.

Autophagy is a highly regulated degradative process crucial for maintaining cell homeostasis. This important catabolic mechanism can be nonspecific, but usually occurs with fine spatial selectivity (compartmentalization), engaging only specific subcellular sites. While the molecular machines driving autophagy are well understood, the involvement of localized signaling events in this process is not well defined. Among the pathways that regulate autophagy, the cyclic AMP (cAMP)/protein kinase A (PKA) cascade can be compartmentalized in distinct functional units called microdomains. However, while it is well established that, depending on the cell type, cAMP can inhibit or promote autophagy, the role of cAMP/PKA microdomains has not been tested. Here we show not only that the effects on autophagy of the same cAMP elevation differ in different cell types, but that they depend on a highly complex sub-compartmentalization of the signaling cascade. We show in addition that, in HT-29 cells, in which autophagy is modulated by cAMP rising treatments, PKA activity is strictly regulated in space and time by phosphatases, which largely prevent the phosphorylation of soluble substrates, while membrane-bound targets are less sensitive to the action of these enzymes. Interestingly, we also found that the subcellular distribution of PKA type-II regulatory PKA subunits hinders the effect of PKA on autophagy, while displacement of type-I regulatory PKA subunits has no effect. Our data demonstrate that local PKA activity can occur independently of local cAMP concentrations and provide strong evidence for a link between localized PKA signaling events and autophagy.

DOI: https://doi.org/10.1038/s41418-021-00761-8
Front Oncol. 2021 ;11 616079

Mitophagy in Pancreatic Cancer.

Yangchun Xie, Jiao Liu, Rui Kang, Daolin Tang.

  Pancreatic ductal adenocarcinoma (PDAC), one of the most aggressive solid malignancies, is characterized by the presence of oncogenic KRAS mutations, poor response to current therapies, prone to metastasis, and a low 5-year overall survival rate. Macroautophagy (herein referred to as autophagy) is a lysosome-dependent degradation system that forms a series of dynamic membrane structures to engulf, degrade, and recycle various cargoes, such as unused proteins, damaged organelles, and invading pathogens. Autophagy is usually upregulated in established cancers, but it plays a dual role in the regulation of the initiation and progression of PDAC. As a type of selective autophagy, mitophagy is a mitochondrial quality control mechanism that uses ubiquitin-dependent (e.g., the PINK1-PRKN pathway) and -independent (e.g., BNIP3L/NIX, FUNDC1, and BNIP3) pathways to regulate mitochondrial turnover and participate in the modulation of metabolism and cell death. Genetically engineered mouse models indicate that the loss of PINK1 or PRKN promotes, whereas the depletion of BNIP3L inhibits oncogenic KRAS-driven pancreatic tumorigenesis. Mitophagy also play a dual role in the regulation of the anticancer activity of certain cytotoxic agents (e.g., rocaglamide A, dichloroacetate, fisetin, and P. suffruticosa extracts) in PDAC cells or xenograft models. In this min-review, we summarize the latest advances in understanding the complex role of mitophagy in the occurrence and treatment of PDAC.

Keywords:  PDAC - pancreatic ductal adenocarcinoma; autophagy; mitophagy; therapy; tumorigenesis

DOI:  https://doi.org/10.3389/fonc.2021.616079
J Invest Dermatol. 2021 Mar 16. pii: S0022-202X(21)00995-7. [Epub ahead of print]

AMPK inhibits mTOR-driven keratinocyte proliferation after skin damage and stress.

Elizabeth D Crane, Wesley Wong, Hui Zhang, Gerard O'Neil, Justin D Crane.

Epidermal keratinocytes rapidly proliferate to repair the skin barrier and a strict control of division is necessary for healthy tissue homeostasis. However, the pathways that restrain proliferation after epidermal stress are not known. AMP-activated protein kinase (AMPK) is an important signaling mediator of energy metabolism previously associated with skin stress and cancer, yet its explicit impact on keratinocyte growth is not known. To examine the requirement of epidermal AMPK in physiologic skin repair, we genetically deleted AMPK within all adult, Keratin 14-expressing keratinocytes of mice. AMPK loss resulted in hyper-proliferation and hyperactive mTOR signaling following acute wounding, UVB exposure, and phorbol ester application. This excessive division could be completely blocked by the mTORC1 inhibitor rapamycin. Moreover, we establish that the diabetes drug metformin depends on AMPK to suppress stress-induced keratinocyte proliferation. Collectively, these findings show that keratinocyte AMPK restrains mTORC1 to control epidermal proliferation after tissue injury.

DOI: https://doi.org/10.1016/j.jid.2020.12.036
Autophagy. 2021 Mar 17.

CREG1 improves the capacity of the skeletal muscle response to exercise endurance via modulation of mitophagy.

HaiXu Song, Xiaoxiang Tian, Dan Liu, Meili Liu, Yanxia Liu, Jing Liu, Zhu Mei, Chenghui Yan, Yaling Han.

  CREG1 (cellular repressor of E1A-stimulated genes 1) is involved in tissue homeostasis and influences macroautophagy/autophagy to protect cardiovascular function. However, the physiological and pathological role of CREG1 in the skeletal muscle is not clear. Here, we established a skeletal muscle-specific creg1 knockout mouse model (creg1;Ckm-Cre) by crossing the Creg1-floxed mice (Creg1fl/fl) with a transgenic line expressing Cre recombinase under the muscle-specific Ckm (creatine kinase, muscle) promoter. In creg1;Ckm-Cre mice, the exercise time to exhaustion and running distance were significantly reduced compared to Creg1fl/fl mice at the age of 9 months. In addition, the administration of recombinant (re)CREG1 protein improved the motor function of 9-month-old creg1;Ckm-Cre mice. Moreover, electron microscopy images of 9-month-old creg1;Ckm-Cre mice showed that the mitochondrial quality and quantity were abnormal and associated with increased levels of PINK1 (PTEN induced putative kinase 1) and PRKN/PARKIN (parkin RBR E3 ubiquitin protein ligase) but reduced levels of the mitochondrial proteins PTGS2/COX2, COX4I1/COX4, and TOMM20. These results suggested that CREG1 deficiency accelerated the induction of mitophagy in the skeletal muscle. Mechanistically, gain-and loss-of-function mutations of Creg1 altered mitochondrial morphology and function, impairing mitophagy in C2C12 cells. Furthermore, HSPD1/HSP60 (heat shock protein 1) (401-573 aa) interacted with CREG1 (130-220 aa) to antagonize the degradation of CREG1 and was involved in the regulation of mitophagy. To the best of our knowledge, this was the first time to demonstrate that CREG1 localized to the mitochondria and played an important role in mitophagy modulation that determined skeletal muscle wasting during the growth process or disease conditions.

Keywords:  CREG1; HSPD1; mitochondria; mitophagy; skeletal muscle

DOI:  https://doi.org/10.1080/15548627.2021.1904488
Oxid Med Cell Longev. 2021 ;2021 6685468

Involvement of Mitochondrial Dynamics and Mitophagy in Sevoflurane-Induced Cell Toxicity.

Ming Li, Jiguang Guo, Hongjie Wang, Yuzhen Li.

General anesthesia is a powerful and indispensable tool to ensure the accomplishment of surgical procedures or clinical examinations. Sevoflurane as an inhalational anesthetic without unpleasant odor is commonly used in clinical practice, especially for pediatric surgery. However, the toxicity caused by sevoflurane has gained growing attention. Mitochondria play a key role in maintaining cellular metabolism and survival. To maintain the stability of mitochondrial homeostasis, they are constantly going through fusion and fission. Also, damaged mitochondria need to be degraded by autophagy, termed as mitophagy. Accumulating evidence proves that sevoflurane exposure in young age could lead to cell toxicity by triggering the mitochondrial pathway of apoptosis, inducing the abnormalities of mitochondrial dynamics and mitophagy. In the present review, we focus on the current understanding of mitochondrial apoptosis, dynamics and mitophagy in cell function, the implications for cell toxicity in response to sevoflurane, and their underlying potential mechanisms.

DOI: https://doi.org/10.1155/2021/6685468
Autophagy. 2021 Mar 17. 1-10

TEX264 at the intersection of autophagy and DNA repair.

John Fielden, Marta Popović, Kristijan Ramadan.

  TEX264 (testes expressed gene 264) is a single-pass transmembrane protein, consisting of an N-terminal hydrophobic region, a gyrase inhibitory (GyrI)-like domain, and a loosely structured C terminus. TEX264 was first identified as an endoplasmic reticulum (ER)-resident Atg8-family-binding protein that mediates the degradation of portions of the ER during starvation (i.e., reticulophagy). More recently, TEX264 was identified as a cofactor of VCP/p97 ATPase that promotes the repair of covalently trapped TOP1 (DNA topoisomerase 1)-DNA crosslinks. This review summarizes the current knowledge of TEX264 as a protein with roles in both autophagy and DNA repair and provides an evolutionary and structural analysis of GyrI proteins. Based on our phylogenetic analysis, we provide evidence that TEX264 is a member of a large superfamily of GyrI-like proteins that evolved in bacteria and are present in metazoans, including invertebrates and chordates.Abbreviations: Atg8: autophagy related 8; Atg39: autophagy related 39; Cdc48: cell division cycle 48; CGAS: cyclic GMP-AMP synthase; DPC: DNA-protein crosslinks; DSB: DNA double-strand break; ER: endoplasmic reticulum; GyrI: gyrase inhibitory domain; LRR: leucine-rich repeat; MAFFT: multiple alignment using fast Fourier transform; MAP1LC3/LC3: microtubule-associated protein 1 light chain 3; MTOR: mechanistic target of rapamycin kinase; STUBL: SUMO targeted ubiquitin ligase; SUMO: small ubiquitin-like modifier; TEX264: testis expressed gene 264; TOP1cc: topoisomerase 1-cleavage complex; UBZ: ubiquitin binding Zn finger domain; VCP: valosin containing protein.

Keywords:  Autophagy; DNA repair; TEX264; gyrase inhibitory-like proteins; nucleophagy; reticulophagy

DOI:  https://doi.org/10.1080/15548627.2021.1894059
Cell Death Differ. 2021 Mar 15.

Characterization of a natural variant of human NDP52 and its functional consequences on mitophagy.

Anthea Di Rita, Daniela F Angelini, Teresa Maiorino, Valerio Caputo, Raffaella Cascella, Mukesh Kumar, Matteo Tiberti, Matteo Lambrughi, Nicole Wesch, Frank Löhr, Volker Dötsch, Marianna Carinci, Pasquale D'Acunzo, Valerio Chiurchiù, Elena Papaleo, Vladimir V Rogov, Emiliano Giardina, Luca Battistini, Flavie Strappazzon.

The role of mitophagy, a process that allows the removal of damaged mitochondria from cells, remains unknown in multiple sclerosis (MS), a disease that is found associated with dysfunctional mitochondria. Here we have qualitatively and quantitatively studied the main players in PINK1-mediated mitophagy in peripheral blood mononuclear cells (PBMCs) of patients with relapsing-remitting MS. We found the variant c.491G>A (rs550510, p.G140E) of NDP52, one of the major mitophagy receptor genes, associated with a MS cohort. Through the characterization of this variant, we discovered that the residue 140 of human NDP52 is a crucial modulator of NDP52/LC3C binding, promoting the formation of autophagosomes in order to drive efficient mitophagy. In addition, we found that in the PBMC population, NDP52 is mainly expressed in B cells and by ensuring efficient mitophagy, it is able to limit the production of the proinflammatory cytokine TNF-α following cell stimulation. In sum, our results contribute to a better understanding of the role of NDP52 in mitophagy and underline, for the first time, a possible role of NDP52 in MS.

DOI: https://doi.org/10.1038/s41418-021-00766-3
FEBS J. 2021 Mar 17.

A Guide To… The Regulation Of Selective Autophagy Receptors.

A Gubas, I Dikic.

  Autophagy is a highly conserved catabolic process cells use to maintain their homeostasis by degrading misfolded, damaged, and excessive proteins, non-functional organelles, foreign pathogens, and other cellular components. Hence, autophagy can be non-selective, where bulky portions of the cytoplasm are degraded upon stress, or a highly selective process, where pre-selected cellular components are degraded. To distinguish between different cellular components, autophagy employs selective autophagy receptors, which will link the cargo to the autophagy machinery, thereby sequestering it in the autophagosome for its subsequent degradation in the lysosome. Autophagy receptors undergo post-translational and structural modifications to fulfil their role in autophagy, or upon executing their role, for their own degradation. We highlight the four most prominent protein modifications - phosphorylation, ubiquitination, acetylation, and oligomerisation - that are essential for autophagy receptor recruitment, function, and turnover. Understanding the regulation of selective autophagy receptors will provide deeper insights into the pathway and open up potential therapeutic avenues.

Keywords:  Autophagy; oligomerisation; phosphorylation; receptor; ubiquitination

DOI:  https://doi.org/10.1111/febs.15824
Cell Death Differ. 2021 Mar 15.

Mitophagy protein PINK1 suppresses colon tumor growth by metabolic reprogramming via p53 activation and reducing acetyl-CoA production.

Kunlun Yin, Jordan Lee, Zhaoli Liu, Hyeoncheol Kim, David R Martin, Dandan Wu, Meilian Liu, Xiang Xue.

Colorectal cancer (CRC) is the third leading cause of cancer-related deaths in the US. Understanding the mechanisms of CRC progression is essential to improve treatment. Mitochondria is the powerhouse for healthy cells. However, in tumor cells, less energy is produced by the mitochondria and metabolic reprogramming is an early hallmark of cancer. The metabolic differences between normal and cancer cells are being interrogated to uncover new therapeutic approaches. Mitochondria targeting PTEN-induced kinase 1 (PINK1) is a key regulator of mitophagy, the selective elimination of damaged mitochondria by autophagy. Defective mitophagy is increasingly associated with various diseases including CRC. However, a significant gap exists in our understanding of how PINK1-dependent mitophagy participates in the metabolic regulation of CRC. By mining Oncomine, we found that PINK1 expression was downregulated in human CRC tissues compared to normal colons. Moreover, disruption of PINK1 increased colon tumorigenesis in two colitis-associated CRC mouse models, suggesting that PINK1 functions as a tumor suppressor in CRC. PINK1 overexpression in murine colon tumor cells promoted mitophagy, decreased glycolysis and increased mitochondrial respiration potentially via activation of p53 signaling pathways. In contrast, PINK1 deletion decreased apoptosis, increased glycolysis, and reduced mitochondrial respiration and p53 signaling. Interestingly, PINK1 overexpression in vivo increased apoptotic cell death and suppressed colon tumor xenograft growth. Metabolomic analysis revealed that acetyl-CoA was significantly reduced in tumors with PINK1 overexpression, which was partly due to activation of the HIF-1α-pyruvate dehydrogenase (PDH) kinase 1 (PDHK1)-PDHE1α axis. Strikingly, treating mice with acetate increased acetyl-CoA levels and rescued PINK1-suppressed tumor growth. Importantly, PINK1 disruption simultaneously increased xenografted tumor growth and acetyl-CoA production. In conclusion, mitophagy protein PINK1 suppresses colon tumor growth by metabolic reprogramming and reducing acetyl-CoA production.

DOI: https://doi.org/10.1038/s41418-021-00760-9
Transl Psychiatry. 2021 Mar 15. 11(1): 165

Inhibition of mTOR signaling by genetic removal of p70 S6 kinase 1 increases anxiety-like behavior in mice.

Muriel Koehl, Elodie Ladevèze, Caterina Catania, Daniela Cota, Djoher Nora Abrous.

The mechanistic target of rapamycin (mTOR) is a ubiquitously expressed kinase that acts through two complexes, mTORC1 and mTORC2, to regulate protein homeostasis, as well as long lasting forms of synaptic and behavioral plasticity. Alteration of the mTOR pathway is classically involved in neurodegenerative disorders, and it has been linked to dysregulation of cognitive functions and affective states. However, information concerning the specific involvement of the p70 S6 kinase 1 (S6K1), a downstream target of the mTORC1 pathway, in learning and memory processes and in the regulation of affective states remains scant. To fill this gap, we exposed adult male mice lacking S6K1 to a battery of behavioral tests aimed at measuring their learning and memory capabilities by evaluating reference memory and flexibility with the Morris water maze, and associative memory using the contextual fear conditioning task. We also studied their anxiety-like and depression-like behaviors by, respectively, performing elevated plus maze, open field, light-dark emergence tests, and sucrose preference and forced swim tests. We found that deleting S6K1 leads to a robust anxious phenotype concomitant with associative learning deficits; these symptoms are associated with a reduction of adult neurogenesis and neuronal atrophy in the hippocampus. Collectively, these results provide grounds for the understanding of anxiety reports after treatments with mTOR inhibitors and will be critical for developing novel compounds targeting anxiety.

DOI: https://doi.org/10.1038/s41398-020-01187-5
Nat Commun. 2021 Mar 19. 12(1): 1782

Molecular basis of V-ATPase inhibition by bafilomycin A1.

Rong Wang, Jin Wang, Abdirahman Hassan, Chia-Hsueh Lee, Xiao-Song Xie, Xiaochun Li.

Pharmacological inhibition of vacuolar-type H+-ATPase (V-ATPase) by its specific inhibitor can abrogate tumor metastasis, prevent autophagy, and reduce cellular signaling responses. Bafilomycin A1, a member of macrolide antibiotics and an autophagy inhibitor, serves as a specific and potent V-ATPases inhibitor. Although there are many V-ATPase structures reported, the molecular basis of specific inhibitors on V-ATPase remains unknown. Here, we report the cryo-EM structure of bafilomycin A1 bound intact bovine V-ATPase at an overall resolution of 3.6-Å. The structure reveals six bafilomycin A1 molecules bound to the c-ring. One bafilomycin A1 molecule engages with two c subunits and disrupts the interactions between the c-ring and subunit a, thereby preventing proton translocation. Structural and sequence analyses demonstrate that the bafilomycin A1-binding residues are conserved in yeast and mammalian species and the 7'-hydroxyl group of bafilomycin A1 acts as a unique feature recognized by subunit c.

DOI: https://doi.org/10.1038/s41467-021-22111-5
Autophagy. 2021 Mar 14. 1-13

Selective autophagy receptor SQSTM1/ p62 inhibits Seneca Valley virus replication by targeting viral VP1 and VP3.

Wei Wen, Xiangmin Li, Mengge Yin, Haoyuan Wang, Liuxin Qin, Hui Li, Wenqiang Liu, Zekai Zhao, Qiongqiong Zhao, Huanchun Chen, Junjie Hu, Ping Qian.

  Macroautophagy/autophagy plays a critical role in antiviral immunity through targeting viruses and initiating host immune responses. The receptor protein, SQSTM1/p62 (sequestosome 1), plays a vital role in selective autophagy. It serves as a receptor targeting ubiquitinated proteins or pathogens to phagophores for degradation. In this study, we explored the reciprocal regulation between selective autophagy receptor SQSTM1 and Seneca Valley virus (SVV). SVV infection induced autophagy. Autophagy promoted SVV infection in pig cells but played opposite functions in human cells. Overexpression of SQSTM1 decreased viral protein production and reduced viral titers. Further study showed that SQSTM1 interacted with SVV VP1 and VP3 independent of its UBA domain. SQSTM1 targeted SVV VP1 and VP3 to phagophores for degradation to inhibit viral replication. To counteract this, SVV evolved strategies to circumvent the host autophagic machinery to promote viral replication. SVV 3Cpro targeted the receptor SQSTM1 for cleavage at glutamic acid 355, glutamine 392, and glutamine 395 and abolished its capacity to mediate selective autophagy. At the same time, the 3Cpro-mediated SQSTM1 cleavage products lost the ability to inhibit viral propagation. Collectively, our results provide evidence for selective autophagy in host against viruses and reveal potential viral strategies to evade autophagic machinery for successful pathogenesis. Abbreviations: Baf.A1: bafilomycin A1; Co-IP: co-immunoprecipitation; hpi: h post-infection; LIR: LC3-interacting region; MAP1LC3B/LC3B: microtubule-associated protein 1 light chain 3 beta; MOI: multiplicity of infection; PB1: N-terminal Phox/Bem1p; Rap.: rapamycin; Seneca Valley virus: SVV; SQSTM1/p62: sequestosome 1; SQSTM1-N355: residues 1 to 355 of SQSTM1; SQSTM1-C355: residues 355 to 478 of SQSTM1; SQSTM1-N392: residues 1 to 392 of SQSTM1; SQSTM1-C392: residues 392 to 478 of SQSTM1; SQSTM1-N388: residues 1 to 388 of SQSTM1; SQSTM1-N397: residues 1 to 397 of SQSTM1; UBA: ubiquitin association; Ubi: ubiquitin.

Keywords:  3C protease; SQSTM1; VP1; VP3; cleavage; selective autophagy

DOI:  https://doi.org/10.1080/15548627.2021.1897223
Dev Cell. 2021 Mar 09. pii: S1534-5807(21)00162-3. [Epub ahead of print]

Rheb mediates neuronal-activity-induced mitochondrial energetics through mTORC1-independent PDH activation.

Wanchun Yang, Dejiang Pang, Mina Chen, Chongyangzi Du, Lanlan Jia, Luoling Wang, Yunling He, Wanxiang Jiang, Liping Luo, Zongyan Yu, Mengqian Mao, Qiuyun Yuan, Ping Tang, Xiaoqiang Xia, Yiyuan Cui, Bo Jing, Alexander Platero, Yanhui Liu, Yuquan Wei, Paul F Worley, Bo Xiao.

  Neuronal activity increases energy consumption and requires balanced production to maintain neuronal function. How activity is coupled to energy production remains incompletely understood. Here, we report that Rheb regulates mitochondrial tricarboxylic acid cycle flux of acetyl-CoA by activating pyruvate dehydrogenase (PDH) to increase ATP production. Rheb is induced by synaptic activity and lactate and dynamically trafficked to the mitochondrial matrix through its interaction with Tom20. Mitochondria-localized Rheb protein is required for activity-induced PDH activation and ATP production. Cell-type-specific gain- and loss-of-function genetic models for Rheb reveal reciprocal changes in PDH phosphorylation/activity, acetyl-CoA, and ATP that are not evident with genetic or pharmacological manipulations of mTORC1. Mechanistically, Rheb physically associates with PDH phosphatase (PDP), enhancing its activity and association with the catalytic E1α-subunit of PDH to reduce PDH phosphorylation and increase its activity. Findings identify Rheb as a nodal point that balances neuronal activity and neuroenergetics via Rheb-PDH axis.

Keywords:  Rheb; mTORC1; mitochondria; neuroenergetics; neuronal activity; pyruvate dehydrogenase

DOI:  https://doi.org/10.1016/j.devcel.2021.02.022
Front Oncol. 2021 ;11 632956

Mechanobiology of Autophagy: The Unexplored Side of Cancer.

Maria Paz Hernández-Cáceres, Leslie Munoz, Javiera M Pradenas, Francisco Pena, Pablo Lagos, Pablo Aceiton, Gareth I Owen, Eugenia Morselli, Alfredo Criollo, Andrea Ravasio, Cristina Bertocchi.

  Proper execution of cellular function, maintenance of cellular homeostasis and cell survival depend on functional integration of cellular processes and correct orchestration of cellular responses to stresses. Cancer transformation is a common negative consequence of mismanagement of coordinated response by the cell. In this scenario, by maintaining the balance among synthesis, degradation, and recycling of cytosolic components including proteins, lipids, and organelles the process of autophagy plays a central role. Several environmental stresses activate autophagy, among those hypoxia, DNA damage, inflammation, and metabolic challenges such as starvation. In addition to these chemical challenges, there is a requirement for cells to cope with mechanical stresses stemming from their microenvironment. Cells accomplish this task by activating an intrinsic mechanical response mediated by cytoskeleton active processes and through mechanosensitive protein complexes which interface the cells with their mechano-environment. Despite autophagy and cell mechanics being known to play crucial transforming roles during oncogenesis and malignant progression their interplay is largely overlooked. In this review, we highlight the role of physical forces in autophagy regulation and their potential implications in both physiological as well as pathological conditions. By taking a mechanical perspective, we wish to stimulate novel questions to further the investigation of the mechanical requirements of autophagy and appreciate the extent to which mechanical signals affect this process.

Keywords:  autophagosome; biomembranes; cytoskeleton; mechanosensing; mechanotransduction

DOI:  https://doi.org/10.3389/fonc.2021.632956
FASEB J. 2021 Apr;35(4): e21456

Reduced nicotinamide mononucleotide is a new and potent NAD+ precursor in mammalian cells and mice.

Rubén Zapata-Pérez, Alessandra Tammaro, Bauke V Schomakers, Angelique M L Scantlebery, Simone Denis, Hyung L Elfrink, Judith Giroud-Gerbetant, Carles Cantó, Carmen López-Leonardo, Rebecca L McIntyre, Michel van Weeghel, Álvaro Sánchez-Ferrer, Riekelt H Houtkooper.

  Nicotinamide adenine dinucleotide (NAD+ ) homeostasis is constantly compromised due to degradation by NAD+ -dependent enzymes. NAD+ replenishment by supplementation with the NAD+ precursors nicotinamide mononucleotide (NMN) and nicotinamide riboside (NR) can alleviate this imbalance. However, NMN and NR are limited by their mild effect on the cellular NAD+ pool and the need of high doses. Here, we report a synthesis method of a reduced form of NMN (NMNH), and identify this molecule as a new NAD+ precursor for the first time. We show that NMNH increases NAD+ levels to a much higher extent and faster than NMN or NR, and that it is metabolized through a different, NRK and NAMPT-independent, pathway. We also demonstrate that NMNH reduces damage and accelerates repair in renal tubular epithelial cells upon hypoxia/reoxygenation injury. Finally, we find that NMNH administration in mice causes a rapid and sustained NAD+ surge in whole blood, which is accompanied by increased NAD+ levels in liver, kidney, muscle, brain, brown adipose tissue, and heart, but not in white adipose tissue. Together, our data highlight NMNH as a new NAD+ precursor with therapeutic potential for acute kidney injury, confirm the existence of a novel pathway for the recycling of reduced NAD+ precursors and establish NMNH as a member of the new family of reduced NAD+ precursors.

Keywords:  NAD+; NMNH; metabolism; nicotinamide mononucleotide

DOI:  https://doi.org/10.1096/fj.202001826R